Despite the proven health benefits of fish oil to the human body, the unpleasant aftertaste and short shelf-life limit the public acceptability as supplementation. Microencapsulation of the fish oil into microspheres is an approach to overcome these limitations. This study aims to prepare controllable-size fish oil alginate microspheres using pulsed electrospray technique for enhancing fish oil stability and palatability. Fish oil alginate microspheres were prepared and optimized by bipolar wave-based drop on demand jetting electrospray. The microspheres were characterized in terms of particle size, aspect ratio, encapsulation efficiency (EE), loading capacity (LC), Fourier transform infrared spectroscopy (FTIR) and drug release. The stability of the fish oil microspheres was assessed based on specific characteristics and antioxidant activity over a period of 6 months. The anticancer effectiveness of encapsulated and unencapsulated fish oil was evaluated using HCT116 and 3T3 cell lines. Additionally, a human panel palatability test was conducted to evaluate the taste masking ability of fish oil microspheres. The optimal formulation exhibited an average particle size of 344.75 ± 10.84 μm, aspect ratio of 1.03 ± 0.02, EE of 98.98 ± 0.72%, and LC of 22.60 ± 0.62%. The FTIR analysis revealed that the chemical properties of the fish oil were preserved after microencapsulation and remained stable after 6 months of storage. The fish oil microspheres showed a superior anticancer effect compared to the free ones. In addition, the panellists of the palatability test of the fish oil microspheres showed an excellent taste masking ability. Hence, this study formulated fish oil microspheres with enhanced stability, efficacy, and palatability, suggesting their potential utility as dietary supplements to fulfil the daily recommended intake of fish oil.